Kinetic proofreading at single molecular level: Aminoacylation of tRNA^{Ile} and the role of water as an editor

Proofreading/editing in protein synthesis is essential for accurate translation of information from the genetic code. In this article we present a theoretical investigation of efficiency of a kinetic proofreading mechanism that employs hydrolysis of the wrong substrate as the discriminatory step in enzyme catalytic reactions. We consider aminoacylation of tRNA^{Ile} which is a crucial step in protein synthesis and for which experimental results are now available. We present an augmented kinetic scheme and then employ methods of stochastic simulation algorithm to obtain time dependent concentrations of different substances involved in the reaction and their rates of formation. We obtain the rates of product formation and ATP hydrolysis for both correct and wrong substrates (isoleucine and valine in our case), in single molecular enzyme as well as ensemble enzyme kinetics. The present theoretical scheme correctly reproduces (i) the amplitude of the discrimination factor in the overall rates between isoleucine and valine which is obtained as (1.8 \times 10^2).(4.33 \times 10^2) = 7.8 \times 10^4, (ii) the rates of ATP hydrolysis for both Ile and Val at different substrate concentrations in the aminoacylation of tRNA^{Ile}. The present study shows a non-michaelis type dependence of rate of reaction on tRNA^{Ile} concentration in case of valine. The editing in steady state is found to be independent of amino acid concentration. Interestingly, the computed ATP hydrolysis rate for valine at high substrate concentration is same as the rate of formation of Ile-tRNA^{Ile} whereas at intermediate substrate concentration the ATP hydrolysis rate is relatively low

Nucleation of a stable solid from melt in the presence of multiple metastable intermediate phases: Wetting, Ostwald step rule and vanishing polymorphs

In many systems, nucleation of a stable solid may occur in the presence of other (often more than one) metastable phases. These may be polymorphic solids or even liquid phases. In such cases, nucleation of the solid phase from the melt may be facilitated by the metastable phase because the latter can "wet" the interface between the parent and the daughter phases, even though there may be no signature of the existence of metastable phase in the thermodynamic properties of the parent liquid and the stable solid phase. Straightforward application of classical nucleation theory (CNT) is flawed here as it overestimates the nucleation barrier since surface tension is overestimated (by neglecting the metastable phases of intermediate order) while the thermodynamic free energy gap between daughter and parent phases remains unchanged. In this work we discuss a density functional theory (DFT) based statistical mechanical approach to explore and quantify such facilitation. We construct a simple order parameter dependent free energy surface that we then use in DFT to calculate (i) the order parameter profile, (ii) the overall nucleation free energy barrier and (iii) the surface tension between the parent liquid and the metastable solid and also parent liquid and stable solid phases. The theory indeed finds that the nucleation free energy barrier can decrease significantly in the presence of wetting. This approach can provide a microscopic explanation of Ostwald step rule and the well-known phenomenon of "disappearing polymorphs" that depends on temperature and other thermodynamic conditions. Theory reveals a diverse scenario for phase transformation kinetics some of which may be explored via modern nanoscopic synthetic methods

Proteostasis collapse is a driver of cell aging and death.

What molecular processes drive cell aging and death? Here, we model how proteostasis-i.e., the folding, chaperoning, and maintenance of protein function-collapses with age from slowed translation and cumulative oxidative damage. Irreparably damaged proteins accumulate with age, increasingly distracting the chaperones from folding the healthy proteins the cell needs. The tipping point to death occurs when replenishing good proteins no longer keeps up with depletion from misfolding, aggregation, and damage. The model agrees with experiments in the worm Caenorhabditis elegans that show the following: Life span shortens nonlinearly with increased temperature or added oxidant concentration, and life span increases in mutants having more chaperones or proteasomes. It predicts observed increases in cellular oxidative damage with age and provides a mechanism for the Gompertz-like rise in mortality observed in humans and other organisms. Overall, the model shows how the instability of proteins sets the rate at which damage accumulates with age and upends a cell's normal proteostasis balance

Polymorph selection during crystallization of a model colloidal fluid with a free energy landscape containing a metastable solid

The free energy landscape responsible for crystallization can be complex even for relatively simple systems like hard sphere and charged stabilized colloids. In this work, using hard-core repulsive Yukawa model, which is known to show complex phase behavior consisting of fluid, FCC and BCC phases, we studied the interplay between the free energy landscape and polymorph selection during crystallization. When the stability of the BCC phase with respect to the fluid phase is gradually increased by changing the temperature and pressure at a fixed fluid-FCC stability, the final phase formed by crystallization is found to undergo a switch from the FCC to the BCC phase, even though FCC remains thermodynamically the most stable phase. We further show that the nature of local bond-orientational order parameter fluctuations in the metastable fluid phase as well as the composition of the critical cluster depend delicately on the free energy landscape, and play a decisive role in the polymorph selection during crystallization

Gas-Liquid Nucleation in Two Dimensional System

We study the nucleation of the liquid phase from a supersaturated vapor in two dimensions (2D). Using different Monte Carlo simulation methods, we calculate the free energy barrier for nucleation, the line tension and also investigate the size and shape of the critical nucleus. The study is carried out at an intermediate level of supersaturation(away from the spinodal limit). In 2D, a large cut-off in the truncation of the Lennard-Jones (LJ) potential is required to obtain converged results, whereas low cut-off (say, $2.5\sigma$ is generally sufficient in three dimensional studies, where $\sigma$ is the LJ diameter) leads to a substantial error in the values of line tension, nucleation barrier and characteristics of the critical cluster. It is found that in 2D, the classical nucleation theory (CNT) fails to provide a reliable estimate of the free energy barrier. It underestimates the barrier by as much as 70% at the saturation-ratio S=1.1 (defined as S=P/PC, where PC is the coexistence pressure at reduced temperature $T^{\star}= 0.427$). Interestingly, CNT has been found to overestimate the nucleation free energy barrier in three dimensional (3D)systems near the triple point. In fact, the agreement with CNT is worse in 2D than in 3D. Moreover, the existing theoretical estimate of the line tension overestimates the value significantly.Comment: 24 pages, 8 figure

Crossover dynamics at large metastability in gas-liquid nucleation

We have developed an alternate description of dynamics of nucleation in terms of an extended set of order parameters. The order parameters consist of an ordered set of kth largest clusters, ordered such that k = 1 is the largest cluster in the system, k = 2 is the second largest cluster, and so on. We have derived an analytic expression for the free energy for the kth largest cluster, which is in excellent agreement with the simulated results. At large supersaturation, the free energy barrier for the growth of the kth largest cluster disappears and the nucleation becomes barrierless. The major success of this extended theoretical formalism is that it can clearly explain the observed change in mechanism at large metastability P. Bhimalapuram et al., Phys. Rev. Lett. 98, 206104 (2007)] and the associated dynamical crossover. The classical nucleation theory cannot explain this crossover. The crossover from activated to barrierless nucleation is found to occur at a supersaturation where multiple clusters cross the critical size. We attribute the crossover as the onset of the kinetic spinodal. We have derived an expression for the rate of nucleation in the barrierless regime by modeling growth as diffusion on the free energy surface of the largest cluster. The model reproduces the slower increase in the rate of growth as a function of supersaturation, as observed in experiments